Baseline information on the water quality status of coral reefs and associated habitats of La Parguera, southwestern PR, is presented. Measurements of temperature, salinity, chlorophyll a, turbidity, fluorescence of dissolved organic matter, bacterial abundance and productivity, bacteriophytoplankton, sedimentation and stable isotopes of particulate organic matter were made at various stations within the area from 2003 through 2005. Significant daily fluctuations were observed at all stations and seasonal changes indicate inputs of materials from terrestrial sources even at the shelf edge. The δ¹³C data indicates low inputs from terrestrial particles (min = -18 ‰ vs. PDB) while variations of dissolved organic matter fluorescence suggest periodic inputs of terrestrially derived matter and nutrients throughout the shelf, though most notable towards the coast. Chlorophyll a (mostly > 0.5µg.l^-1), bacteria (ca. 1 ×10⁶ cells.ml^-1) and bacteriophytoplankton (72-122 ×10³ cell.ml^-1) indicate the presence of significant nutrient inputs while particle δ¹⁵N shows minimum to moderate enrichment from anthropogenic sources (max = 3.5 ‰ vs. air). Sedimentation rates were mostly <100 g.m^-2.d^-1, being higher during stormy conditions. Significant co-variation between turbidity and sedimentation was observed to be useful for modeling sedimentation patterns. Higher levels of the different water quality indictors were observed closer to the coast.